CrispRVariants (version 1.0.2)

narrowAlignments: Narrow a set of aligned reads to a target region

Description

Aligned reads are narrowed to the target region. In the case of reads with deletions spanning the boundaries of the target, reads are narrowed to the start of the deletion,

Usage

narrowAlignments(alns, target, ...)
"narrowAlignments"(alns, target, ..., reverse.complement, verbose = FALSE)

Arguments

alns

A GAlignments object including a metadata column "seq" containing the sequence

target

A GRanges object

...

additional arguments

reverse.complement

Should the aligned reads be reverse complemented?

verbose

(Default: FALSE)

Value

The narrowed alignments (GAlignments),

Examples

bam_fname <- system.file("extdata", "gol_F1_clutch_2_embryo_4_s.bam",
                         package = "CrispRVariants")
bam <- GenomicAlignments::readGAlignments(bam_fname, use.names = TRUE)
target <- GenomicRanges::GRanges("18", IRanges::IRanges(4647377, 4647399),
          strand = "+")
narrowAlignments(bam, target, reverse.complement = FALSE)